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Zinc in PDB 1d5j: Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor.

Enzymatic activity of Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor.

All present enzymatic activity of Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor.:
3.4.24.17;

Protein crystallography data

The structure of Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor., PDB code: 1d5j was solved by N.G.Almstead, R.S.Bradley, S.Pikul, B.De, M.G.Natchus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.780, 78.540, 105.270, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 25.7

Other elements in 1d5j:

The structure of Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor. also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor. (pdb code 1d5j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor., PDB code: 1d5j:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1d5j

Go back to Zinc Binding Sites List in 1d5j
Zinc binding site 1 out of 4 in the Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:11.0
occ:1.00
OB A:MM3401 1.8 20.0 1.0
OA A:MM3401 1.9 2.0 1.0
NE2 A:HIS201 2.1 6.3 1.0
NE2 A:HIS211 2.3 2.8 1.0
NE2 A:HIS205 2.4 5.1 1.0
C A:MM3401 2.6 15.5 1.0
NA A:MM3401 2.8 9.5 1.0
CD2 A:HIS201 3.1 5.5 1.0
CE1 A:HIS201 3.2 6.0 1.0
CD2 A:HIS211 3.2 3.2 1.0
CD2 A:HIS205 3.3 9.3 1.0
CE1 A:HIS211 3.3 2.0 1.0
CE1 A:HIS205 3.5 2.0 1.0
OE2 A:GLU202 3.7 7.6 1.0
C13 A:MM3401 4.0 16.7 1.0
CG A:HIS201 4.3 3.6 1.0
ND1 A:HIS201 4.3 3.6 1.0
ND1 A:HIS211 4.4 2.0 1.0
CG A:HIS211 4.4 4.2 1.0
CG A:HIS205 4.5 7.1 1.0
ND1 A:HIS205 4.5 2.0 1.0
C6 A:MM3401 4.6 2.0 1.0
CD A:GLU202 4.6 2.0 1.0
C5 A:MM3401 4.8 3.9 1.0
OE1 A:GLU202 4.8 10.1 1.0
CE A:MET219 4.9 2.0 1.0
C14 A:MM3401 4.9 15.5 1.0
N12 A:MM3401 4.9 14.2 1.0

Zinc binding site 2 out of 4 in 1d5j

Go back to Zinc Binding Sites List in 1d5j
Zinc binding site 2 out of 4 in the Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:12.8
occ:1.00
ND1 A:HIS179 2.0 4.3 1.0
NE2 A:HIS151 2.0 2.9 1.0
NE2 A:HIS166 2.1 13.0 1.0
OD2 A:ASP153 2.1 9.4 1.0
CE1 A:HIS179 2.9 2.8 1.0
CE1 A:HIS151 3.0 6.5 1.0
CD2 A:HIS166 3.0 12.9 1.0
CD2 A:HIS151 3.1 5.5 1.0
CG A:ASP153 3.1 16.6 1.0
CG A:HIS179 3.1 4.4 1.0
CE1 A:HIS166 3.1 13.5 1.0
OD1 A:ASP153 3.3 23.9 1.0
CB A:HIS179 3.6 4.8 1.0
NE2 A:HIS179 4.0 2.0 1.0
OH A:TYR168 4.1 6.6 1.0
ND1 A:HIS151 4.1 2.0 1.0
CG A:HIS151 4.2 4.2 1.0
CD2 A:HIS179 4.2 2.0 1.0
CG A:HIS166 4.2 9.1 1.0
ND1 A:HIS166 4.3 9.7 1.0
O A:TYR155 4.3 14.9 1.0
CB A:ASP153 4.4 15.0 1.0
CZ A:PHE157 4.6 2.6 1.0
CE1 A:TYR168 4.7 3.9 1.0
CZ A:TYR168 4.9 2.5 1.0
O A:HOH403 4.9 9.3 1.0
CE1 A:PHE157 5.0 3.0 1.0
CE2 A:PHE157 5.0 3.3 1.0

Zinc binding site 3 out of 4 in 1d5j

Go back to Zinc Binding Sites List in 1d5j
Zinc binding site 3 out of 4 in the Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:34.6
occ:1.00
OB B:MM3901 1.9 29.0 1.0
OA B:MM3901 1.9 20.6 1.0
NE2 B:HIS701 2.2 8.6 1.0
NE2 B:HIS711 2.2 20.4 1.0
NE2 B:HIS705 2.2 10.7 1.0
C B:MM3901 2.5 24.3 1.0
NA B:MM3901 2.6 21.3 1.0
CD2 B:HIS705 3.0 11.7 1.0
CE1 B:HIS701 3.1 9.3 1.0
CD2 B:HIS711 3.1 19.6 1.0
CE1 B:HIS711 3.2 18.7 1.0
CD2 B:HIS701 3.2 11.7 1.0
CE1 B:HIS705 3.3 11.1 1.0
C13 B:MM3901 3.9 24.0 1.0
CG B:HIS705 4.2 9.0 1.0
OE2 B:GLU702 4.3 12.7 1.0
ND1 B:HIS705 4.3 5.8 1.0
ND1 B:HIS711 4.3 22.3 1.0
ND1 B:HIS701 4.3 9.3 1.0
CG B:HIS711 4.3 20.5 1.0
CG B:HIS701 4.3 9.9 1.0
C6 B:MM3901 4.4 24.1 1.0
C1 B:MM3901 4.6 19.9 1.0
C14 B:MM3901 4.8 20.4 1.0
C5 B:MM3901 4.9 23.7 1.0
N12 B:MM3901 5.0 22.7 1.0

Zinc binding site 4 out of 4 in 1d5j

Go back to Zinc Binding Sites List in 1d5j
Zinc binding site 4 out of 4 in the Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:14.7
occ:1.00
OD2 B:ASP653 2.0 14.9 1.0
NE2 B:HIS666 2.0 10.1 1.0
ND1 B:HIS679 2.1 5.6 1.0
NE2 B:HIS651 2.3 11.2 1.0
CE1 B:HIS666 3.0 7.0 1.0
CE1 B:HIS679 3.0 5.0 1.0
CG B:HIS679 3.0 6.7 1.0
CD2 B:HIS651 3.0 9.4 1.0
CG B:ASP653 3.0 13.4 1.0
CD2 B:HIS666 3.1 7.6 1.0
CE1 B:HIS651 3.4 11.6 1.0
CB B:HIS679 3.4 8.5 1.0
OD1 B:ASP653 3.5 18.7 1.0
NE2 B:HIS679 4.0 4.3 1.0
O B:TYR655 4.0 15.0 1.0
CD2 B:HIS679 4.1 7.8 1.0
ND1 B:HIS666 4.1 7.8 1.0
CG B:HIS666 4.2 5.8 1.0
CG B:HIS651 4.3 7.9 1.0
CB B:ASP653 4.3 7.3 1.0
OH B:TYR668 4.4 14.9 1.0
ND1 B:HIS651 4.4 8.2 1.0
CZ B:PHE657 4.6 3.2 1.0
CE1 B:PHE657 4.7 7.4 1.0
CE1 B:TYR668 4.8 12.2 1.0
CA B:HIS679 4.9 7.5 1.0

Reference:

N.G.Almstead, R.S.Bradley, S.Pikul, B.De, M.G.Natchus, Y.O.Taiwo, F.Gu, L.E.Williams, B.A.Hynd, M.J.Janusz, C.M.Dunaway, G.E.Mieling. Design, Synthesis, and Biological Evaluation of Potent Thiazine- and Thiazepine-Based Matrix Metalloproteinase Inhibitors. J.Med.Chem. V. 42 4547 1999.
ISSN: ISSN 0022-2623
PubMed: 10579818
DOI: 10.1021/JM990330Y
Page generated: Mon Jan 25 16:08:18 2021

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